This can happen when studio attempts to build an assembly file that has been renamed to *.x in a pre 2.0 project. For instance:
avr32-gcc -x assembler-with-cpp -c -mpart=ap7000 \ -I../src/SOFTWARE_FRAMEWORK/UTILS/PREPROCESSOR \ -I../src/SOFTWARE_FRAMEWORK/UTILS \ -osrc\SOFTWARE_FRAMEWORK\DRIVERS\INTC\exception.o \ ..\src\SOFTWARE_FRAMEWORK\DRIVERS\INTC\exception.x
Notice that mpart is the default value ap7000 while it should have been uc3b0256es. In order to fix this, go to project properties and change the part to another value then back again.